I've been developing a PHP web-based application for over a year now and it's starting to get massive - basically, to large to just keep making the small changes and uploading - we are beginning to lose track of where we're at with version control etc....

is there any good software you guys have used for monitoring checkpoints, version control, change log etc...

We use Microsoft Project for project management. For configuration management there are tools like CVS, PVCS Tracker. We use a suite of tools called Razor but it only runs on Unix/Linux as far as I am aware.